Question: vcf-consensus outputs sequence same as reference
0
gravatar for seretnacho
2.8 years ago by
seretnacho0
seretnacho0 wrote:

I downloaded a fasta file with a consensus sequence and a vcf file with the variant for certain individual (both files from 1000 genomes). I'm trying to get the sequence for that individual. To do that, i'm using vcf-consensus like this (let's say the consensus is master.fasta and the vcf is HG02291.vcf.gz):

tabix -p vcf HG02291.vcf.gz
cat master.fasta | vcf-consensus HG02291.vcf.gz > HG02291.fasta

After I do that, I compare HG02291.fasta with master.fasta and they are the exact same files (same headers and sequences), therefore vcf-consensus is not applying any changes to master.fasta. I've tried the same procedure with many other samples and it still does not work. What am I doing wrong?

ADD COMMENTlink modified 24 months ago by rajesh.msch0 • written 2.8 years ago by seretnacho0
1
gravatar for liangjiao.xue
2.8 years ago by
liangjiao.xue100
United States
liangjiao.xue100 wrote:

Here are two clues to consider:

1) Make sure the *vcf.gz file was zipped using bgzip. You could unzip them first and zip them again with bgzip from tabix
2) Make sure the chromosome IDs are same in VCF and fasta. Sometimes, it's "chr01" in one file, but "chr1" or "1" in another one.

ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by liangjiao.xue100
0
gravatar for rajesh.msch
24 months ago by
rajesh.msch0 wrote:

i checked it twice but still showing problem> same output as reference fasta file

ADD COMMENTlink written 24 months ago by rajesh.msch0

Please use ADD COMMENT to answer to earlier reaction, as such this thread remains logically structured and easy to follow.

ADD REPLYlink written 24 months ago by WouterDeCoster36k

Not a solution but I would recommend trying - a) rerunning with -s <sample_name> -i options b) running vcf-validator to check vcf

ADD REPLYlink written 24 months ago by microfuge970

i checked it twice but still showing problem> same output as reference fasta file

ADD REPLYlink written 24 months ago by rajesh.msch0

Did you figured out what it was? Coz I'm struggling with the same.

ADD REPLYlink written 4 months ago by Susmita Mandal20
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